Extraction of oils from castor bean (Ricinus communis L.) and Jatropha curcas L. to produce biofuel is set to increase. The produced seed cake could be applied to soil as it is nutrient rich, but might affect soil functioning. Seven soils from Chiapas, México, were amended with seed cake of both plants while CO 2 , CH 4 and N 2 O emissions and mineral N concentrations were monitored in an aerobic incubation. The concentration of phorbol esters in the J. curcas seed cake (JSC) was 0.993 mg/g while no ricin was detected in the R. communis seed cake (RSC). Application of JSC increased CO 2 emission 2.5-times, N 2 O 12.6-times and CH 4 18.4-times compared to the unamended soil, while RSC CO 2 emission 2.1-times, N 2 O 21.3-times and CH 4 2.3-times. On average, 66% of the 88 mg organic N added with JSC was mineralized and 83% of the 101 mg organic N of the RSC within 56 days. It was found that J. curcas and castor bean seed cake increased CO 2 , CH 4 and N 2 O emission and mineral N in soil, without inhibiting soil microbial activity.